This project will develop and investigate small molecules for inhibition of specific protein functions. The design of these inhibitors and analysis of their effects on protein function will define how change sin protein structure relate to corresponding changes in function. This collaborative effort will draw on expertise in enzymology, chemistry, structural biology, and molecular modeling to design, prepare and assay these molecules. Compounds that show initial promise will be further optimized through combinatorial library development of more diverse structures. Our specific target include helicase and tubulin, and these are the two specific aims: I. Structure and Function Analysis of NS3 Helicase Through Inhibitor Development. The goal of this research is to design inhibitors for the Hepatitis C virus NS3 helicase using a rationally designed combinatorial approach. The research will also provide structure/function and kinetic mechanistic information on the helicase and its model of translocation of single-stranded DNA. II. Designed Ligands for Tubulin and Tubulin-binding Protein Cofactors. The goals of this project are to prepare anti-mitotic agents based on the eleutherobin and astrogorgin scaffolds, and to develop ligands which inhibit tubulin assembly by binding to tubulin-binding cofactors or cofactor-tubulin complexes.